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Detailed information for vg0726337284:

Variant ID: vg0726337284 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26337284
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


GATCCCCTACCAAGTAGAGTTGGCCAAATCTATATCATCCATTGTTTTCTACGGCTGAGATTATGCCTCATTAAATTTACCTAATAAAGTAACTCCTCAA[C/T]
ATTAATGGTTATAGCTTGATAGGAAAATTAGTTTTTTCAACGCTTCCTCTATTTTGATTATGTTCTCATTTGTTCTTAATAAACACATACAGTCGATCAA

Reverse complement sequence

TTGATCGACTGTATGTGTTTATTAAGAACAAATGAGAACATAATCAAAATAGAGGAAGCGTTGAAAAAACTAATTTTCCTATCAAGCTATAACCATTAAT[G/A]
TTGAGGAGTTACTTTATTAGGTAAATTTAATGAGGCATAATCTCAGCCGTAGAAAACAATGGATGATATAGATTTGGCCAACTCTACTTGGTAGGGGATC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.70% 44.20% 0.13% 0.00% NA
All Indica  2759 81.40% 18.40% 0.22% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.00% 0.00% NA
Aus  269 93.70% 6.30% 0.00% 0.00% NA
Indica I  595 93.80% 6.10% 0.17% 0.00% NA
Indica II  465 93.50% 6.50% 0.00% 0.00% NA
Indica III  913 66.80% 32.70% 0.44% 0.00% NA
Indica Intermediate  786 81.70% 18.20% 0.13% 0.00% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 43.30% 56.70% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0726337284 C -> T LOC_Os07g44070.1 upstream_gene_variant ; 2844.0bp to feature; MODIFIER silent_mutation Average:77.784; most accessible tissue: Callus, score: 99.162 N N N N
vg0726337284 C -> T LOC_Os07g44070.2 upstream_gene_variant ; 2844.0bp to feature; MODIFIER silent_mutation Average:77.784; most accessible tissue: Callus, score: 99.162 N N N N
vg0726337284 C -> T LOC_Os07g44060-LOC_Os07g44070 intergenic_region ; MODIFIER silent_mutation Average:77.784; most accessible tissue: Callus, score: 99.162 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0726337284 C T -0.02 0.01 -0.01 -0.03 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726337284 NA 1.32E-11 mr1636 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 NA 3.19E-08 mr1806 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 NA 1.00E-15 mr1968 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 NA 1.01E-06 mr1063_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 NA 4.02E-12 mr1258_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 3.20E-08 3.20E-08 mr1261_2 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 NA 1.75E-06 mr1275_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 NA 1.10E-06 mr1574_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 NA 2.11E-07 mr1607_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 NA 1.74E-10 mr1806_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 NA 6.89E-21 mr1968_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0726337284 NA 3.63E-11 mr1986_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251